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A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome

To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we develop high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF b...

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Autores principales: Rhie, Suhn Kyong, Perez, Andrew A., Lay, Fides D., Schreiner, Shannon, Shi, Jiani, Polin, Jenevieve, Farnham, Peggy J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742760/
https://www.ncbi.nlm.nih.gov/pubmed/31515496
http://dx.doi.org/10.1038/s41467-019-12079-8
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author Rhie, Suhn Kyong
Perez, Andrew A.
Lay, Fides D.
Schreiner, Shannon
Shi, Jiani
Polin, Jenevieve
Farnham, Peggy J.
author_facet Rhie, Suhn Kyong
Perez, Andrew A.
Lay, Fides D.
Schreiner, Shannon
Shi, Jiani
Polin, Jenevieve
Farnham, Peggy J.
author_sort Rhie, Suhn Kyong
collection PubMed
description To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we develop high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer-promoter loop anchors. We also find that the chromatin structure surrounding the androgen receptor (AR) locus is altered in the prostate cancer cells with many cancer-specific enhancer-promoter loops. This creation of 3D epigenomic maps enables a better understanding of prostate cancer biology and mechanisms of gene regulation.
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spelling pubmed-67427602019-09-16 A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome Rhie, Suhn Kyong Perez, Andrew A. Lay, Fides D. Schreiner, Shannon Shi, Jiani Polin, Jenevieve Farnham, Peggy J. Nat Commun Article To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we develop high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer-promoter loop anchors. We also find that the chromatin structure surrounding the androgen receptor (AR) locus is altered in the prostate cancer cells with many cancer-specific enhancer-promoter loops. This creation of 3D epigenomic maps enables a better understanding of prostate cancer biology and mechanisms of gene regulation. Nature Publishing Group UK 2019-09-12 /pmc/articles/PMC6742760/ /pubmed/31515496 http://dx.doi.org/10.1038/s41467-019-12079-8 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Rhie, Suhn Kyong
Perez, Andrew A.
Lay, Fides D.
Schreiner, Shannon
Shi, Jiani
Polin, Jenevieve
Farnham, Peggy J.
A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome
title A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome
title_full A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome
title_fullStr A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome
title_full_unstemmed A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome
title_short A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome
title_sort high-resolution 3d epigenomic map reveals insights into the creation of the prostate cancer transcriptome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742760/
https://www.ncbi.nlm.nih.gov/pubmed/31515496
http://dx.doi.org/10.1038/s41467-019-12079-8
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